Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 4 | 16.88 |
PPRS is classified as low-risk (≤4), medium-risk (4-6), and high-risk (≥6).
Antibiotic resistance genes
Comprehensive Antibiotic Resistance Database (CARD)
| Query ID | Begin | End | ARO name | ARO accession | CARD name | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| LLPHFKPL_1 | 3095364 | 3096218 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
| LLPHFKPL_1 | 3066160 | 3067362 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| LLPHFKPL_1 | 2840162 | 2841331 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| LLPHFKPL_1 | 1865132 | 1865449 | ykkD | ARO:3003064 | ykkD | 97.14 | 100.00 | AL009126.1 |
| LLPHFKPL_1 | 1864794 | 1865132 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| LLPHFKPL_1 | 1405110 | 1407680 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 100.00 | AL009126.3 |
| LLPHFKPL_1 | 1115468 | 1117114 | vmlR | ARO:3004476 | vmlR | 98.91 | 100.18 | NC_000964.3 |
| LLPHFKPL_1 | 864903 | 865496 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
| LLPHFKPL_1 | 814347 | 815780 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.00 | JYFL01000006.1 |
| LLPHFKPL_1 | 801535 | 802455 | mphK | ARO:3004541 | mphK | 96.41 | 100.00 | CP010314.1 |
RGI v6.0.3 (Database: CARD Variants v4.0.2, Nov. 2023 release)
ResFinder
| Query ID | Begin | End | Resistance gene | Phenotype | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|
| LLPHFKPL_1 | 3095364 | 3096218 | aadK | Streptomycin | 98.60 | 100.00 | M26879 |
| LLPHFKPL_1 | 492369 | 493745 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 98.47 | 100.00 | D12567 |
| LLPHFKPL_1 | 801535 | 802455 | mph(K) | Spiramycin, Telithromycin | 96.75 | 99.89 | NC_000964 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| LLPHFKPL_1 | 1115471 | 1117114 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.91 | 100.00 | WP_003234144.1 |
| LLPHFKPL_1 | 492372 | 493745 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.69 | 100.00 | WP_063856081.1 |
| LLPHFKPL_1 | 3095367 | 3096218 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| LLPHFKPL_1 | 801535 | 802452 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 96.41 | 100.00 | WP_003246254.1 |
| LLPHFKPL_1 | 489819 | 490337 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| LLPHFKPL_1 | 2541411 | 2544008 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.83 | 100.00 | WP_087347987.1 |
AMRFinderPlus v4.0.3 (Database: Oct. 2024 release)
Virulence factors
Virulence Factor Database (VFDB)
| Query ID | qstart | qend | Gene name | e-value | VF name | VF category | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|---|
| LLPHFKPL_1 | 4065522 | 4066703 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| LLPHFKPL_1 | 3657974 | 3658759 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.62 | 100.00 | NP_391080 |
| LLPHFKPL_1 | 2637323 | 2637964 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| LLPHFKPL_1 | 4065058 | 4065507 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| LLPHFKPL_1 | 4063897 | 4065039 | capA | 0.0 | Capsule | Immune modulation | 99.12 | 100.00 | NP_391469 |
| LLPHFKPL_1 | 3656752 | 3657948 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.08 | 100.00 | NP_391079 |
| LLPHFKPL_1 | 2491993 | 2493756 | dep/capD | 0.0 | Capsule | Immune modulation | 98.92 | 100.00 | NP_389723 |
| LLPHFKPL_1 | 3655104 | 3656723 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.83 | 100.00 | NP_391078 |
| LLPHFKPL_1 | 3646982 | 3654118 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.53 | 100.00 | NP_391076 |
| LLPHFKPL_1 | 3654138 | 3655076 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.40 | 100.00 | NP_391077 |
BLASTN v2.16.0 (Database: VFDB, Dec. 2024 release)
VirulenceFinder
| Query ID | Begin | End | Database | Virulence factor | Protein function | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| No hit found | ||||||||
VirulenceFinder v2.0. 4 (Database: virulencefinder_db, Feb . 2024 release)
Pathogenic genes
PHI-base
| Query ID | qstart | qend | Gene name | e-value | Function | Identity | Coverage | Gene ID |
|---|---|---|---|---|---|---|---|---|
| LLPHFKPL_1 | 650895 | 652031 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| LLPHFKPL_1 | 537272 | 538141 | pdxS | 3.03e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LLPHFKPL_1 | 2175964 | 2176740 | CodY | 3.31e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LLPHFKPL_1 | 3909638 | 3910207 | ClpP | 2.46e-98 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)
Plasmid
PlasmidFinder
| Query ID | Begin | End | Plasmid | Query / Template | Identity | Accession no. |
|---|---|---|---|---|---|---|
| No hit found | ||||||
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| LLPHFKPL_1 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LLPHFKPL_1 | 1808907 | 1835264 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG4612, VOG4705 |
| LLPHFKPL_1 | 3018991 | 3041412 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773 |
Phigaro v2.4.0 (Database: Jan. 2024 release)